Soil microbial carbon use efficiency (CUE) has been identified as a critical parameter in regulating soil organic carbon (SOC) sequestration. Climate change has been shown in numerous studies to increase the input of root exudates into the soil, thereby affecting soil communities and soil carbon (C) balance. However, it remains uncertain how citric acid (a major component of root exudates) impacts the microbial CUE in forest soil under different soil fertility conditions. Hence, we investigated the responses of soil microbial community composition, enzyme activity, and microbial CUE to a 2-year citric acid addition and mineral fertilization experiment in the rhizospheres of Abies fargesii var. faxoniana and Picea purpurea. Citric acid addition had no significant effects on the C: nutrient imbalance between microbial biomass and their resources in fertilized soils, but it increased the microbial C: nutrient imbalance in non-fertilized soils. The effects of citric acid on microbial CUE were influenced by soil fertility. Citric acid addition had a significant negative effect on microbial CUE in non-fertilized soils in both species tested, whereas no significant change in this parameter was observed in soil treated with NPK fertilizers. NPK fertilization can reduce citric acid-induced soil C loss by increasing microbial CUE. The microbial CUE of P. purpurea was lower than that of A. faxoniana. The differences in root C allocation, the C:N ratio of fine root and root exudates, and N uptakes may contribute to tree species variation in microbial CUE. Our findings contribute to a better understanding of the processes governing the impacts of C and nutrient inputs on microbial C cycles in subalpine conifer forest soils.